Note that in the PDF referenced they write:
"The bell housing must be aligned within 0.012 inches of runout. If the transmission is not in line with the crank shaft, there will be a bind on the input shaft causing the transmission to shift poorly." I personally believe that failure to align the bell housing properly is the cause of 98% of the transmission shifting complaints on this forum, regardless of the manufacturer. When I was up at ERA many moons ago, it literally took them the better part of a day to get my Lakewood aligned, doweled, and bolted up to my FE. And that was with the engine on a stand, not in the car. This point can't be emphasized enough when your drive train is being put together.